Download opal zip file :
opal.tgz
You must have Java version ≥ 5
(aka v1.5)
for Opal versions 0.9.x and up (Java ≥ 1.4 for earlier Opal versions).
Read the documentation page for further instructions.
You may also download the
ISMB paper.
Version History
Current Stable Version
opal_2.1.3.tgz (05/16/13)
- Recompiled 2.1.2 to run with Java 1.5 or 1.6. Previously only ran on 1.7
Latest Beta Version
opal_3.1.b0.tgz (06/14/16)
- Added support for Adaptive Local Realignment (see the Facet website)
- Added documentation for adaptive local realignment and parameter advising
The development version of Opal v3 can be found at Github (http://git.io/Opal).
Previous Versions (placed here for the sake of posterity; no reason to use them)
opal_3.0.b0.tgz (08/03/15)
- Added the ability of run multiple alignments with different configurations in parallel
- Added Facet estimator, which can be calculated when given predicted structure
- Allows for advising using Facet (parameter advising sets can be found on the Facet website)
- Allows user to specify replacement matrix other then BLOSUM62, either one one several built in matrices or as file input.
opal_2.1.2.tgz (08/30/13)
- Fixed shell script to work on OS X (and BSD)
- Fixed error mode raised by alignments of a very large number of sequences due
to number overflow (identified by Nam Nguyen)
opal_2.1.1.tgz (01/15/13)
- Missing source code for some modules, now added to tgz file
opal_2.1.0.tgz (01/18/12)
- Missing 00README file added to .tgz file
- added --mem flag to shell script
- Slight memory reduction in multiple alignment
opal_2.0.0.tgz (01/11/11)
- Added a shell script that runs Opal.jar with appropriate Java flags
- Bundled in a .tgz file
- Enabled methods for incorporating predicted protein secondary structure,
including development of a script to control psipred
Opal.1.0.3.jar (06/24/09)
Fixes error when guide tree is provided. Previous version would iterate, building a new tree (and crash along the way).
Opal.1.0.2.jar (02/25/09)
Correctly handles windows newline characters in fasta files.
Opal.1.0.1.jar (02/13/09)
Reduced peak memory consumption by roughly 40%.
Opal.1.0.0.jar (01/06/09)
The first official release, coincident with it's release
in Mesquite.
Several interface and logging changes to accomodate inclusion in Mesquite.
Opal.0.9.3.jar (11/11/08)
Includes support for nucleotide sequences
Opal.0.9.2.jar (10/31/08)
Opal.0.9.1.jar (10/30/08)
Opal.0.3.7.jar (10/17/07)
Opal.0.3.6.jar (09/06/07)
Opal.0.3.5.jar (08/31/07)
Opal was originally implemented as a C program (Why switch to Java? Read this).
Download opal as a zipped or tar/gzipped archive:
opal_0.2.0.tar.gz (05/08/07)
opal_0.2.0.zip
To unpackage the files, run
gzip -dc opal_0.2.0.tar.gz | tar -xvf -
or
unzip opal_0.2.0.zip
To compile and run opal, do the following:
cd alignalign
make all
cd ../opal
make all
./Opal -f your_file